It just keeps coming back to software, doesn't it.... or configuration. And I am in no way disputing your abilities, you seem to know what your doing. I know this, when I edit the config.txt file using Notepad in Windows I find it very difficult to edit the file contents, so I use Notepad++ v6.9 as that lays everything out in a more editable format, nothing like the config.txt file loaded into Notepad.
Your using a Mac right?
Which I know next to nothing about, but... could it be the editor program your using messing up the config.txt file?
But then, Volumio wouldn't work either, would it... to quote hondagx35,
"this is strange and shouldn't happen." And your using the latest version,
"RuneAudio_rpi2_rp3_0.4-beta_20160321_2GB"? Maybe try an earlier version, maybe.
"Both LEDs are lit up." <--- So the card is getting power and the driver for the card is being loaded.
Try this link, maybe it'll help (if it don't help, it won't hurt):
https://www.youtube.com/watch?v=blO3EtP_D10